PTSDBrainomics CELLxGENE Census 2024-07-01 cutoff 0 MADs 5

Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Explain with AI

        Configure AI settings to get explanations of plots and data in this report.

        Keys entered here will be stored in your browser's local storage. See the docs.

        Anonymize samples off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
        Settings are automatically saved. You can also save named configurations below.

        Save Settings

        You can save the toolbox settings for this report to the browser or as a file.

        Load Settings

        Choose a saved report profile from the browser or load from a file:

          Load from File

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.28

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        PTSDBrainomics CELLxGENE Census 2024-07-01 cutoff 0 MADs 5

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the PavlidisLab/sc-annotation-pipeline analysis pipeline.
        Report generated on 2025-09-22, 13:54 PDT based on data in: /space/grp/rschwartz/rschwartz/cell_annotation_cortex.nf/work/1a/f1aa455dd379e8284ba01081b8935f/PTSDBrainomics

        Sample cell type composition

        Composition per sample of predicted cell types.

        Created with MultiQC

        Leiden cluster composition (cell types)

        Leiden clustering performed on log-transformed data with top 2000 variable genes, 10 PCs, 30 neighbors, resolution = 0.3.

        Created with MultiQC

        Cell type markers

        Expression of select markers. Count are averaged across cell-type labels and z-score normalized across genes.

        Created with MultiQC

        Cell type UMAP

        UMAP of the cell type labels, sample names and leiden clusters.

        PTSDBrainomics | sc31 outliers

        PTSDBrainomics | sc43 upset

        PTSDBrainomics | sc1 outliers

        PTSDBrainomics | sc1 upset

        PTSDBrainomics | sc33 upset

        PTSDBrainomics | sc18 outliers

        PTSDBrainomics | sc33 outliers

        PTSDBrainomics | sc3 outliers

        PTSDBrainomics | sc44 outliers

        PTSDBrainomics | sc11 upset

        PTSDBrainomics | sc2 outliers

        PTSDBrainomics | sc32 outliers

        PTSDBrainomics | sc34 outliers

        PTSDBrainomics | sc13 upset

        PTSDBrainomics | sc42 outliers

        PTSDBrainomics | sc21 outliers

        PTSDBrainomics | sc5 outliers

        PTSDBrainomics | sc35 outliers

        PTSDBrainomics | sc43 outliers

        PTSDBrainomics | sc3 upset

        PTSDBrainomics | sc31 upset

        PTSDBrainomics | sc44 upset

        PTSDBrainomics | sc6 outliers

        PTSDBrainomics | sc6 upset

        PTSDBrainomics | sc34 upset

        PTSDBrainomics | sc7 outliers

        PTSDBrainomics | sc21 upset

        PTSDBrainomics | sc7 upset

        PTSDBrainomics | sc35 upset

        PTSDBrainomics | sc2 upset

        PTSDBrainomics | sc11 outliers

        PTSDBrainomics | sc18 upset

        PTSDBrainomics | sc12 outliers

        PTSDBrainomics | sc12 upset

        PTSDBrainomics | sc13 outliers

        PTSDBrainomics | sc32 upset

        PTSDBrainomics | sc42 upset

        PTSDBrainomics | sc5 upset

        MultiQC v1.28 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.